Command Line Tools (CWL)
1.0.0
1.0.0
  • MSK-ACCESS command-line tools
  • ABRA2
    • v2.17
    • v2.22
  • access_utils
    • 0.1.1
  • bcftools
    • bcftools bgzip v1.15.1
    • bcftools concat v1.15.1
    • bcftools norm v1.15.1
    • bcftools sort v1.15.1
    • bcftools tabix v1.15.1
  • Bedtools
    • genomecov v2.28.0_cv2
    • merge v2.28.0_cv2
    • sortbed v2.28.0_cv2
  • Biometrics
    • extract
    • minor
    • major
    • genotype
    • sexmismatch
  • Delly
    • delly call 0.9.1
    • delly call 1.0.3
  • Disambiguate
    • v1.0.0
  • Fastp
    • 0.20.1
    • 0.24.0
  • Fgbio
    • CallDuplexConsensusReads v1.2.0
    • CollectDuplexSeqMetrics v1.2.0
    • GroupReadsByUmi v1.2.0
    • FastqToBam v1.2.0
    • FilterConsensusReads v1.2.0
    • simplex_filter v0.1.8
  • GATK
    • ApplyBQSR v4.1.2.0
    • ApplyBQSR v4.1.8.1
    • BaseRecalibrator v4.1.2.0
    • BaseRecalibrator v4.1.8.1
    • MergeBamAlignment v4.1.8.0
    • MergeSamFiles v4.1.8.0
    • SamToFastq v4.1.8.0
  • GetBaseCountsMultiSample
    • 1.2.5
  • Manta
    • Manta v1.5.1
  • Marianas
    • Collapsing First Pass v1.8.1
    • Collapsing Second Pass v1.8.1
    • Process Loop UMI v1.8.1
    • Seprate BAMs v1.8.1
  • MultiQC
    • MultiQC v1.10.1.7
    • MultiQC v1.12
  • MuTect
    • MuTect 1.1.5
  • Merge Fastq
    • v0.1.7
  • Mosdepth
    • 0.3.3
  • Octopus
    • v0.7.4
  • Oncokb_annotator
    • v3.2.2
  • Picard Tools
    • AddOrReplaceReadGroups v1.96
    • AddOrReplaceReadGroups v2.21.2
    • AddOrReplaceReadGroups v4.1.8.1
    • CollectAlignmentSummaryMetrics v2.8.1
    • CollectAlignmentSummaryMetrics v2.21.2
    • CollectMultipleMetrics v2.8.1
    • CollectMultipleMetrics v2.21.2
    • FixMateInformation v1.96
    • FixMateInformation v2.21.2
    • FixMateInformation v4.1.8.1
    • HSmetrics v2.8.1
    • HSmetrics v2.21.2
    • MarkDuplicates v1.96
    • MarkDuplicates v2.8.1
    • MarkDuplicates v2.21.2
    • MarkDuplicates v4.1.8.1
  • Postprocessing variant calls
    • vardict_filter_case-control 0.1.5
    • vardict_filter_single-sample 0.1.5
    • maf_annotated_by_bed_0.2.2
    • maf_annotated_by_tsv_0.2.3
    • maf_filter_cmoch_0.2.3
    • maf_tag_cmoch_0.2.3
    • maf_annotated_by_bed_0.2.3
  • sequence_qc
    • v0.2.4
  • SnpSift
    • v5.0
  • Trim Galore
    • v0.6.2
  • Ubuntu utilites
    • v18.04
  • VarDictJava
    • v1.8.2
  • VCF2MAF
    • 1.6.21
  • Waltz
    • CountReads v3.1.1
    • PileupMetrics v3.1.1
Powered by GitBook
On this page
Edit on GitHub

Marianas

Collapsing First Pass v1.8.1Collapsing Second Pass v1.8.1Process Loop UMI v1.8.1Seprate BAMs v1.8.1
PreviousManta v1.5.1NextCollapsing First Pass v1.8.1

Last updated 3 years ago